Taxonomic assignment report

Department of Agriculture, Fisheries and Forestry logo
Facility Hogwarts
Analyst John Doe
Analysis started 2025-04-03 05:23:58
Analysis completed 2025-04-03 05:23:58
Wall time 0:0:0 hours

Sample details

locus COI
preliminary_id Phoridae
taxa_of_interest Megaselia scalaris
country India
host Fish meal
sample_id VE25-1434_COI
Query DNA sequence

Result overview

Inconclusive
The analyst should attempt subjective species identification at the genus level.
Reasoning - Flag 1D: At least one candidate species matched with moderate stringency (identity ≥93.5% and <98.5%).

Preliminary morphology ID confirmed NA

Inconclusive taxonomic identity (Flag 1D)

Taxa of interest ruled out False

Flag 2A: Taxon of interest NOT detected

Flag 5.1A: The given locus for this taxon is well represented in reference database (>5 entries)

Flag 5.2B: 10-90% of related taxa have reference sequence(s) at the given locus

Analyst evaluation

Identification of candidate species

Flag 1D: The analyst should attempt subjective species identification at the genus level
At least one candidate species matched with moderate stringency (identity ≥93.5% and <98.5%)

Candidate hits must meet ONE of these criteria:

Minimum alignment length 400bp
Minimum query coverage 85.0%

Candidate hits are then classified as follows:

Classification Alignment identity Number of hits Number of species
STRONG MATCH ≥ 98.5% 0 0
MODERATE MATCH ≥ 93.5% 7 1
NO MATCH < 93.5%

Hits per candidate species (top 10 candidates only)

Species Hits Identity E-value
Dohrniphora cornuta 7 97.89999999999999% 0.0

Analyst evaluation

Taxa of interest

This sections shows the taxa of interest specified by the submitter. Each of these taxa has been cross-referenced against the candidate species to determine if they might match the taxonomic identity of the sample. A blank row indicates a TOI that did not match any candidate species, meaning that it is unlikely that the sample matches that TOI.

Taxon of interest Match rank Match taxon Match species Match accession Match identity
Megaselia scalaris - - - - -

See the Database coverage section to see database coverage for taxa of interest.

Reference sequence source diversity

This analysis evaluates how many independent sources have contributed to reference sequences for each candidate species. This provides a measure of confidence in the taxonomic annotation of references sequences. A sequence that has been annotated by multiple independent sources is more likely to have a correct taxonomic annotation.

Analyst evaluation

Independent sources

Flag 4A: Reference sequences are from diverse sources and therefore likely to be reliable
Reasoning: Matching sequence records for this species are from >5 independent sources (found 6 sources)

6 Independent Sources

The matching reference sequences for this species have been annotated by 6 independent source(s). A source is considered independent if the author list or publication title is distinct.

Source 1

Hit accession Automated Authors Title Journal
MG947378 False Moskowitz,N.A.
Roland,A.B.
Fischer,E.K.
Ranaivorazo,N.
Aguilar,M.T.
Caldera,S.M.
Chea,J.
Cristus,M.
Crowds,J.P.
Demessie,B.
Desjardins-Park,C.R.
Effenberger,A.H.
Flores,F.
Giles,M.
He,E.Y.
Izmaylov,N.S.
Lee,C.
Nadeem,B.
Pagel,N.A.
Phu,K.
Rosen,L.U.
Seda,D.A.
Shen,Y.
Vargas,S.
Weiss,H.S.
Murray,A.W.
Abebe,E.
Vidoudez,C.
Trauger,S.A.
Vences,M.
O'Connell,L.A.
Seasonal changes in diet influences toxicity in the Climbing Mantella frog (Mantella laevigata) Unpublished
MG947378 False Moskowitz,N.
Abebe,E.
Desjardins-Park,C.
He,E.
Rosen,L.
Seda,D.
Caldera,S.
Aguilar,M.
Lee,C.
Izmaylov,N.
Phu,K.
Weiss,H.
Direct Submission Submitted (13-FEB-2018) Biology, Stanford University, 371 Serra Mall, Stanford, CA 94305, USA

Source 2

Hit accession Automated Authors Title Journal
HQ984503 False iBOL Data Release Unpublished
HQ984503 False Direct Submission Submitted (24-JAN-2011) Biodiversity Institute of Ontario, University of Guelph, 50 Stone Rd West, Guelph, Ontario N1G2W1, Canada

Source 3

Hit accession Automated Authors Title Journal
KR666968 False Hebert,P.D.
Ratnasingham,S.
Zakharov,E.V.
Telfer,A.C.
Levesque-Beaudin,V.
Milton,M.A.
Pedersen,S.
Jannetta,P.
deWaard,J.R.
Counting animal species with DNA barcodes: Canadian insects Philos. Trans. R. Soc. Lond., B, Biol. Sci. 371 (1702) (2016) In press
KR666968 False Hebert,P.D.N.
Ratnasingham,S.
Zakharov,E.V.
Dewaard,J.R.
Direct Submission Submitted (11-MAY-2015) Biodiversity Institute of Ontario, University of Guelph, 50 Stone Road EAST, Guelph, Ontario N1G2W1, Canada
KR659695 False Hebert,P.D.
Ratnasingham,S.
Zakharov,E.V.
Telfer,A.C.
Levesque-Beaudin,V.
Milton,M.A.
Pedersen,S.
Jannetta,P.
deWaard,J.R.
Counting animal species with DNA barcodes: Canadian insects Philos. Trans. R. Soc. Lond., B, Biol. Sci. 371 (1702) (2016) In press
KR659695 False Hebert,P.D.N.
Ratnasingham,S.
Zakharov,E.V.
Dewaard,J.R.
Direct Submission Submitted (11-MAY-2015) Biodiversity Institute of Ontario, University of Guelph, 50 Stone Road EAST, Guelph, Ontario N1G2W1, Canada

Source 4

Hit accession Automated Authors Title Journal
MG293276 False Dewaard,J.R. BIOUG Archive GGBN Data Release Unpublished
MG293276 False Dewaard,J.R. Direct Submission Submitted (30-OCT-2017) Collections, Centre for Biodiversity Genomics, 50 Stone Road East, Guelph, Ontario N1G 2W1, Canada

Source 5

Hit accession Automated Authors Title Journal
JQ941749 False Wang,J.-F.
Sheng,X.-X.
Liu,G.-C.
DNA-based identification on sexual dimorphism of Phoridae (Diptera) from China Unpublished
JQ941749 False Wang,J.-F.
Sheng,X.-X.
Liu,G.-C.
Direct Submission Submitted (16-APR-2012) Shenyang University, Liaoning Key Laboratory of Urban Integrated Pest Management and Ecological Security, 21 Wanghua South Street, Dadong District, Shenyang, Liaoning 110044, P.R. China

Source 6

Hit accession Automated Authors Title Journal
MN832849 False Feng,D.
Li,J.
The complete mitochondrial genome of two scuttle flies, Megaselia spiracularis Schmitz and Dohrniphora cornuta (Bigot) (Diptera: Phoridae) Unpublished
MN832849 False Feng,D.
Li,J.
Direct Submission Submitted (14-DEC-2019) College of Life Science and Engineering, Shenyang University, Shenyang University, No. 21, Wanghua South Street, Dadong District, Shenyang, Liaoning 110044, China

Database coverage of target taxa

The target taxa include candidate species, the preliminary morphology ID, and any taxa of interest provided by the submitter. Each of these taxa are independently evaluated against the reference database to determine whether sufficient reference data exists to support identification of the target taxon. Insufficient coverage of a taxon can result in that taxon not be correctly identified as the taxonomic identity of the sample. For example, if the sample is Homo sapiens, but Homo sapiens sequences are not included in the reference database, the analysis will be unable to identity Homo sapiens as the correct taxonomic identity, and will most likely assign the closest relative with reference data as the taxonomic identity.

Analyst evaluation

Database coverage

Flag 5.2B: The database has some support for species in this genus
Reasoning: 10-90% of related taxa have reference sequence(s) at the given locus


Database coverage of Dohrniphora cornuta

Flag 5.1A: The reference data supports this taxon well
Reasoning: The given locus for this taxon is well represented in reference database (>5 entries)

15 records

There are 15 sequences in the reference database for Dohrniphora cornuta at the given locus COI.

Map of database coverage

Database coverage of species in genus Dohrniphora

Flag 5.2B: The database has some support for species in this genus
Reasoning: 10-90% of related taxa have reference sequence(s) at the given locus

/ (%) sequence records were found in the reference database for:

  • Species in the genus Dohrniphora
  • At the target locus COI

Number of GenBank records at locus COI


Database coverage of species in genus Dohrniphora that occur in country of origin

Flag 5.3C: Probability that a different related species from the country of origin is the true taxonomic identity: LOW
Reasoning: No species in genus have been observed in the country of origin

/ (%) sequence records were found in the reference database for:

  • Species in the genus Dohrniphora
  • At the target locus COI
  • In the sample country of origin India

Number of GenBank records at locus COI

Database coverage

Flag 5.1NA: This taxon could not be fully assessed
Reasoning: Assessment of related species is only possible for taxa at rank genus/species


Database coverage of Phoridae

Flag 5.1NA: This taxon could not be fully assessed
Reasoning: Assessment of related species is only possible for taxa at rank genus/species

NA records

There are NA sequences in the reference database for Phoridae at the given locus COI.

Map of database coverage

Database coverage

Flag 5.2B: The database has some support for species in this genus
Reasoning: 10-90% of related taxa have reference sequence(s) at the given locus


Database coverage of Megaselia scalaris

Flag 5.1A: The reference data supports this taxon well
Reasoning: The given locus for this taxon is well represented in reference database (>5 entries)

48 records

There are 48 sequences in the reference database for Megaselia scalaris at the given locus COI.

Map of database coverage

Database coverage of species in genus Megaselia

Flag 5.2B: The database has some support for species in this genus
Reasoning: 10-90% of related taxa have reference sequence(s) at the given locus

/ (%) sequence records were found in the reference database for:

  • Species in the genus Megaselia
  • At the target locus COI

Number of GenBank records at locus COI


Database coverage of species in genus Megaselia that occur in country of origin

Flag 5.3A: Probability that a different related species from the country of origin is the true taxonomic identity: LOW
Reasoning: All species in genus from country of origin have reference sequence(s) for this locus

/ (%) sequence records were found in the reference database for:

  • Species in the genus Megaselia
  • At the target locus COI
  • In the sample country of origin India

Number of GenBank records at locus COI

Intraspecies diversity

This section provides a phylogeny of the candidate reference sequences. The analyst can use this to make a subjective observation on how well the reference sequences are able to distinguish between species. If the phylogeny shows distinct clades for each species, we can be confident that the molecular data are capable of distinguishing between those species. However, if the phylogeny shows overlap between species, this reduces the capacity of the molecular data to confidently distinguish between those species. In some cases, we may see the query sequence falling outside of the adjacent species' clades, which indicates that our query species is not represented in the reference database, which could indicate a rare or novel species.

Analyst evaluation

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The phylogetic tree was constructed with FastME using the Neighbor-Joining method. Multiple-sequence alignment of the candidate reference sequences was performed using MAFFT. The visualization is rendered with TidyTree.

Taxonomy Check

The following resources can be used to ensure that the given taxonomy is legitimate and current.

Taxa Database
General GBIF
General ITIS
Mealybugs & scale ScaleNet database
Thrips Thripswiki
Spider Mites Spider Mites Database
Psocodea (Barklice, Booklice, and Parasitic Lice) Psocodea Species File Online
Orthoptera Orthoptera Species File Online
Drosophilidae TaxoDros
Diptera Catalog of the Diptera of the Australasian and Oceanian Regions
Systema Dipterorum
Aphids Aphid Species File
Ants AntWeb
AntCat
Lepidoptera (butterflies and moths) The Global Lepidoptera Names Index
Gracillariidae (primitive moths) Global Taxonomic Database of Gracillariidae
Pyralidae (pyralid moths) Global Information System on Pyraloidea
Tortricidae (tortrix moths) Tortricidae Resources on the Net